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comparison bgc_calib.xml @ 3:689d7a46e359 draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 03e7755bd0554044c4ca46c27007ee03a58b8d89
author ecology
date Fri, 13 Jun 2025 14:11:41 +0000
parents 6f66f964d64c
children c15538b093e0
comparison
equal deleted inserted replaced
2:6f66f964d64c 3:689d7a46e359
1 <tool id="tool_biogeochemical_calibration" name="BioGeoChemical calibration" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" license="MIT"> 1 <tool id="tool_biogeochemical_calibration" name="BioGeoChemical calibration" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" license="MIT">
2 <description>for sensors according to Argo recommendations</description> 2 <description>for sensors according to Argo recommendations</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">1.0</token> 4 <token name="@VERSION@">1.0</token>
5 <token name="@VERSION_SUFFIX@">0.1</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <container type="docker">easyqcvbgc/easy-qcv_calibration-methods_tool:@VERSION@</container> 8 <container type="docker">easyqcvbgc/easy-qcv_calibration-methods_tool:@VERSION@</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
14 mkdir -p '/runtime/data-in-ref/' && 14 mkdir -p '/runtime/data-in-ref/' &&
15 mkdir -p '/runtime/data-out/' && 15 mkdir -p '/runtime/data-out/' &&
16 mkdir -p ./outputs && 16 mkdir -p ./outputs &&
17 17
18 #for $i, $infile in enumerate($input_raw): 18 #for $i, $infile in enumerate($input_raw):
19 cp '$infile' '/runtime/data-in-raw/${infile.element_identifier}.nc' && 19 #set real_name = $infile.element_identifier
20 #end for 20 #set extension = $real_name.split('.')[-1]
21 #if $extension == 'nc':
22 cp '${infile.file_name}' "/runtime/data-in-raw/${infile.element_identifier}" &&
23 #else
24 cp '${infile.file_name}' "/runtime/data-in-raw/${infile.element_identifier}.nc" &&
25 #end if
26 #end for
21 #if $input_ref: 27 #if $input_ref:
22 #for $i, $infile in enumerate($input_ref): 28 #for $i, $infile in enumerate($input_ref):
23 cp '$infile' '/runtime/data-in-ref/${infile.element_identifier}' && 29 cp '$infile' '/runtime/data-in-ref/${infile.element_identifier}' &&
24 #end for 30 #end for
25 #end if 31 #end if
39 #if $config.type == 'yes': 45 #if $config.type == 'yes':
40 #for $i, $file in enumerate($config.section_config): 46 #for $i, $file in enumerate($config.section_config):
41 default : 47 default :
42 file_name_list_raw: 48 file_name_list_raw:
43 #for $i, $infile in enumerate($input_raw): 49 #for $i, $infile in enumerate($input_raw):
44 #set name_raw='${infile.element_identifier}.nc' 50 #set real_name = $infile.element_identifier
51 #set extension = $real_name.split('.')[-1]
52 #if $extension == 'nc':
53 #set name_raw='${infile.element_identifier}'
54 #else:
55 #set name_raw='${infile.element_identifier}.nc'
56 #end if
45 - ${name_raw} 57 - ${name_raw}
46 #end for 58 #end for
47 param : nitrate 59 param : nitrate
48 param_qc : 60 param_qc :
49 bad : '${param_qc_bad}' 61 bad : '${param_qc_bad}'
50 to_be_replaced : '${param_qc_toreplaced}' 62 to_be_replaced : '${param_qc_toreplaced}'
51 replaced_by : '${param_qc_replacedby}' 63 replaced_by : '${param_qc_replacedby}'
52 calib_configs : 64 calib_configs :
53 - number : 1 65 - number : '${i}'
54 method_raw : 66 method_raw :
55 name : method1 67 name : method1
56 options : 68 options :
57 bypass_P : '${file.bypass.p_value}' 69 bypass_P : '${file.bypass.p_value}'
58 P : '${file.bypass.p_value}' 70 P : '${file.bypass.p_value}'
196 <output_collection name="nc_files" type="list" count="1"/> 208 <output_collection name="nc_files" type="list" count="1"/>
197 <output_collection name="png_files" type="list" count="4"/> 209 <output_collection name="png_files" type="list" count="4"/>
198 </test> 210 </test>
199 </tests> 211 </tests>
200 <help><![CDATA[ 212 <help><![CDATA[
201 ====================== 213 ==========================
202 ODV collection manager 214 BioGeoChemical calibration
203 ====================== 215 ==========================
204 216
205 **What it does** 217 **What it does**
206 218
207 This tool present two type of actions : 219 This tool calibrates BioGeoChemical (BGC) data measured by ARGO or GLIDER network. The BGC variables managed by the tool for the moment are :
208 220
209 - qualificiation & validation : the tool merges various datasets with a common vocabulary and creates a single generic ODV spreadsheet following ODV user’s guide (v5.7.0) in an automatic way. 221 - NITRATE using methods published in `archimer <https://archimer.ifremer.fr/doc/00350/46121/>`
222
210 223
211 **Input description** 224 **Input description**
212 225
213 - file_name_raw : nc file to be qualified 226 - file_name_raw : nc file to be qualified
214 - file_name_ref : nc file used for validation / comparison. noted NULL if no files 227 - param_qc$bad : qc values to be removed from param before calibration
215 - odv_collection$qc_convention : tool makes mapping when its necessary and when global attribute qc_convention is available and filled in file_name_raw 228 - param_qc$to_be_replaced : raw qc values to be replaced for building the adjusted qc values
216 - tool_option$subsetting : 1 apply a subbsetting to ref data searching the smallest box (default) / 0 no subsetting / -1 apply an inverse subseting 229 - param_qc$replaced_by : good qc value replacing raw qc values for building adjusted qc values
217 - tool_option$plt : figure option to see the subseted box (0 or 1) - default name subset_box.png 230 - method_raw$name which method/equation will be used for estimating the adjusted variable
218 231 - method_raw$options :
219 with default values different from NULL : 232 - bypass_P : 0 (tool defines the P of reference for adjustment ) OR 1 (user defines P and chooses P below)
220 233 - P : NULL (if bypass_P = 0) OR numeric_values (if bypass_P = 1)
221 - odv_collection$name : odv_collection.txt 234 - multiple_linear_regression : 0 (automatic choice of N) or 1 (single linear regression) or N>1 (N linear regressions)
222 - odv_collection$qc_convention : ARGO 235 - single_favored : FALSE or TRUE to favored the single linear regression
223 - tool_action : 236 - method_ref$name : which kind of reference method (for example model or climatology) will be used by the method_raw for estimating the adjusted variable.
224 - tool_option$subsetting : 237 - reference : which reference method like canyonb or woa will be used by the method_raw for estimating the adjusted variable.
225 - tool_option$plt : 238
226 239 If the list of raw file name is empty, the tool stops If the user makes an error in the file extension, tool changes it by itself. If the user misses the yaml configuration, tool uses its default config and upload available files in data-in-raw
227 If the list of raw file name is empty, tool stops If the user make an error in the file extension, tool changes it by itself. If the user miss the yaml configuration, tool uses its default config and upload file in data-in-raw and data-in-ref 240
228 241 compatibility matrix
242
243 - variable / application mode / [method_raw.name, method_ref.name, reference]
244 - nitrate / R_APP_CN / [method1, model, canyon_b] & [method1, model, canyon_med] & [method1, clim, woa]
245
229 **Output** 246 **Output**
230 247
231 This tool creates a single generic ODV spreadsheet following ODV user’s guide 248 - an extended nc file including the _adjusted and _adjusted_qc
249 - figures helping to understand the adjustment
232 250
233 ]]></help> 251 ]]></help>
234 <citations> 252 <citations>
235 <citation type="bibtex"> 253 <citation type="bibtex">
236 @Manual{, 254 @Manual{,